Troubleshooting Server Lag and Crashes
Here are the steps you will need to take to trouble your minecraft server if you are experiencing lag or constant minecraft server crashes:
1) If you are running a Bukkit server, STOP your server and disable ALL your plugins. If you use a plugin like World Guard to protect your server you will want to backup your current map and start a temporary map) If you are running a DEV or BETA build of craftbukkit, disable bukkit and switch to official minecraft.
2) Now that all you plugins are disabled restart your server and login again. If the lag is gone this indicates one or more of your plugins is causing the lag. You will need to start enabling your plugins one at a time until you find the plugin that is causing the lag on your server, just make sure to stop an start your server each time you enable a plugin again. To see if a plugin is performing poorly you can look in your server.log file in your "minecraft" folder on your server, any plugin that shows a SEVERE error in the server log should be disabled. (older logs can be found in the "minecraft/Logs" folder).
3) If you have disabled all your plugins and the lag is still present on your server you will then need to try a temporary map. STOP you server and backup your current map in McMyAdmin. See this guide here on how to create a backup in McMyAdmin. Now that your current map is backed up you may remove your current map to do so go to the "Backups" tab and select "Delete World". (Note all this must be done while your server is turned off.) Once you have removed your current world, restart your server and a new map will generate. When you login again please allow a few minutes for the new map to be created.
4) If you have disabled all your plugins and tried a temporary map for about 30 minutes and are still seeing lag on your server you will need to try a traceroute using this guide here. Also you can check our Network Issues page here to see if we are currently experiencing any issues at our end. Also make sure to try our test server @ test.minecraft.ms and see if you lag there or not.
5) If you are still stuck with lag after all these steps please open a support ticket and send us the results of your traceroute.
Note: 95% of all lag and server crashes are caused by either Bukkit plugins or a corrupt map. Isolating the offending plugins and the map is the first step in finding the cause of lag on your server.